R Under development (unstable) (2024-02-05 r85863 ucrt) -- "Unsuffered Consequences"
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> library(pcalg)
> possible_p <- c(seq(10,30,by=10))
> possible_neighb_size <- c(3:10)
> 
> num_setings <-10
> num_rep <- 2
> 
> ##amount of bg knowledge in percent
> p_bg <- seq(0,1,by=0.1)
> 
> counterr <- 0
> 
> seed1 <- 1 
> for (r in seed1:num_setings) {
+   set.seed(r)
+   ##Then we can choose one setting:
+   p <-  sample(possible_p,1)
+   neigh <- sample(possible_neighb_size,1)
+   prob <- round(neigh/(p-1),3)
+ 
+   ## cat("r=",r,", p=",p,", nb=",neigh,"\n")     
+   
+   ## then for every setting selected we can generate i.e. 20 graph
+   for (d in 1: num_rep){
+     ##i left the seed inside for now
+     ## i am not sure which seed option makes it easier for us
+     ## feel free to move this around
+     #seed <- sample(possible_seed,1)
+     #set.seed(seed)
+     
+     ##get graph
+     g <- pcalg:::randomDAG(p, prob)  ## true DAG
+     cpdag <- dag2cpdag(g) ## true CPDAG
+     
+     ## get adjacency matrix
+     cpdag.amat <- t(as(cpdag,"matrix"))
+     dag.amat <- t(as(g,"matrix"))
+     dag.amat[dag.amat != 0] <- 1
+ 
+     amat.cpdag <- cpdag.amat
+     if (!isValidGraph(amat.cpdag,type="cpdag")){
+       counterr <- counterr +1
+     }
+     if (!isValidGraph(dag.amat,type="dag")){
+       counterr <- counterr +1
+     }
+   }
+ }
> counterr
[1] 0
> 
> amat <- matrix(c(0,1,0, 0,0,1, 0,0,0), 3,3)
> colnames(amat) <- rownames(amat) <- letters[1:3]
> ## graph::plot(as(t(amat), "graphNEL"))             
> stopifnot(isValidGraph(amat = amat, type = "dag"), ## is a valid DAG
+   !isValidGraph(amat = amat, type = "cpdag"), ## is a valid CPDAG 
+   isValidGraph(amat = amat, type = "pdag") ) ## is a valid PDAG
> 
> ## a -- b -- c
> amat <- matrix(c(0,1,0, 1,0,1, 0,1,0), 3,3)
> colnames(amat) <- rownames(amat) <- letters[1:3]
> ## plot(as(t(amat), "graphNEL"))             
> stopifnot(!isValidGraph(amat = amat, type = "dag"), ## not a valid DAG
+   isValidGraph(amat = amat, type = "cpdag"), ## is a valid CPDAG
+   isValidGraph(amat = amat, type = "pdag") )## is a valid PDAG
> 
> ## a -- b -- c -- d -- a
> amat <- matrix(c(0,1,0,1, 1,0,1,0, 0,1,0,1, 1,0,1,0), 4,4)
> colnames(amat) <- rownames(amat) <- letters[1:4]
> ## plot(as(t(amat), "graphNEL"))             
> stopifnot(!isValidGraph(amat = amat, type = "dag"),  ## not a valid DAG
+   !isValidGraph(amat = amat, type = "cpdag"), ## not a valid CPDAG
+   !isValidGraph(amat = amat, type = "pdag") ) ## not a valid PDAG
> 
> proc.time()
   user  system elapsed 
   1.78    0.15    1.92